Hydrographic data from the OPTOMA program OPTOMA20 OPTOMA20 P 16 March 1986 OPTOMA20 Leg MI 24 March - 3 April 1986 OPTOMA20 Leg MII 7 - 15 April 1986 OPTOMA20 Leg D 25 April - 6 May 1986

THe OPTOMA (Ocean Prediction Through Observation, Modeling, and Analysis) Program a joint NPS/Harvard program sponsored by ONR, seeks to understand the mesoscale (fronts, eddies, and jets) variability and dynamics of the California Current System and to determine the scientific limits to practical mesoscale ocean forecasting. To help carry out the aims of this project, a series of cruises has been planned in two subdomains, NOCAL and CENCAL, Three cruises were undertaken during March, April and May 1986: two (Legs Ml and Mll) on the NOAA ship Mc AUTHOR, one (Leg D) on the USNS DE STEIGUER. In addition, one P-3 overflight (Leg P) was made one week before the first cruise. Leg P, on 16 March, sampled a domain approximately 240km square centered about 280 km off the coast between Pt. Arena and Cape Mendocino, with additional transects from and to San Francisco, Leg Ml was carried out from 24 March to 3 April (Figure 8), Leg Mll from 7 to 15 April (Figure 20), and Leg D from 25 April to 6 May (Figure 32). Each cruise sampled the same domain as Leg P. On these cruises, oceanographic stations were occupied at approximately 18km along each trackPrepared for: Office of Naval Research Environmental Sciences Directoratehttp://archive.org/details/hydrographicdata008cianN0001486WR24027NAApproved for public release; distribution is unlimited

Hydrographic data from the OPTOMA program OPTOMA21 7 - 20 July 1986

The OPTOMA (Ocean Prediction Through Observation, Modeling and Analysis) program, a joint NPS/Harvard program sponsored by ONR, seeks to understand the mesoscale (fronts, eddies, and jets) variability and dynamics of the California current systems and to determine the scientific limits to practical mesoscale ocean forecasting. To help carry out the aims of this project a series of cruises has been planned two subdomains, nocal and cencal. Optoma21 was a multidisciplinary study which took place from 7 to 20 July 1986 aboard the R/V Point Sur in the nocal domain. In addition to conducting a quasi- synoptic CTD/XBT mapping of a cool anomaly, meandering jet, and eddy system, measurements were made to determine: 1) the fine scale variability of the upper ocean mass and velocity fields; 2) the upper ocean nutrient, optical and phytoplankton fields; and 3) the structure of the zooplankton population. In this report, the CTD/XBT data are presentedresearch project "Ocean Prediction Through Observation, Modeling and Analysis" sponsored by the Physical Oceanography Program of the Office of Naval Research under Program Element 61153N.http://archive.org/details/hydrographicda20jul86wittN000146WR24027NAApproved for public release; distribution is unlimited

Hydrographic data from the OPTOMA Program: OPTOMA12, 8-18 October 1984, OPTOMA13, 22 October-3 November 1984, OPTOMA13P, 27 October 1984, OPTOMA14, 3-14 November 1984

The three cruises, OPTOMA12, OPTOMA13, and 0PT0MA14, and one AXBT flight, 0PT0MA13P, were under taken in October and November, 1984. This report presents the hydrographic data, acquired by XBT, AXBT and CTD casts, from the cruises and the flight."Ocean Prediction Through Observations, Modeling and Analysis" sponsored by the Physical Oceanography Program of the Office of Naval Research under Program Element 61153N.http://archive.org/details/hydrographicdata012wittN0001484NR24501NAApproved for public release; distribution is unlimited

A compilation of observations from moored current meters and thermographs (and of complementary oceanographic and atmospheric data). Vol. 2. Oregon continental shelf, August-September 1966

A summary of one phase of a direct observational program conducted in the coastal region off Oregon is presented. The measurements were made primarily on the continental shelf in late coastal upwelling season (August and September 1966). The principal measurements were time series of horizontal current velocity and temperature fields; these observations were made with an array of moored, recording meters. Supplementary measurements of hydrographic variables, wind, atmospheric pressure, and mean sea level were also made. The emphasis of this data report is on the graphical and tabular display of first-order statistics. Limited descriptive remarks are made in order to provide some interpretation for these initial results. More thorough analyses and discussions of the observations are expected to follow from this stage of analysis. In brief, this set of measurements in the coastal upwelling frontal zone indicates the flow field: is highly variable on the time scale of tidal-like motions to that of motions with several-day periods. ii) has a southerly mean at a depth of 20 meters (in the "surface layer"). iii) has a northerly mean at a depth of 60 meters (at the base of the "permanent pycnocline"), has a marked response to variations in the wind field on the time scale of several days. Recommendations regarding future observations and analyses are made

Scaling properties of protein family phylogenies

One of the classical questions in evolutionary biology is how evolutionary processes are coupled at the gene and species level. With this motivation, we compare the topological properties (mainly the depth scaling, as a characterization of balance) of a large set of protein phylogenies with a set of species phylogenies. The comparative analysis shows that both sets of phylogenies share remarkably similar scaling behavior, suggesting the universality of branching rules and of the evolutionary processes that drive biological diversification from gene to species level. In order to explain such generality, we propose a simple model which allows us to estimate the proportion of evolvability/robustness needed to approximate the scaling behavior observed in the phylogenies, highlighting the relevance of the robustness of a biological system (species or protein) in the scaling properties of the phylogenetic trees. Thus, the rules that govern the incapability of a biological system to diversify are equally relevant both at the gene and at the species level.Comment: Replaced with final published versio

Functional determinants for general self-adjoint extensions of Laplace-type operators resulting from the generalized cone

In this article we consider the zeta regularized determinant of Laplace-type operators on the generalized cone. For {\it arbitrary} self-adjoint extensions of a matrix of singular ordinary differential operators modelled on the generalized cone, a closed expression for the determinant is given. The result involves a determinant of an endomorphism of a finite-dimensional vector space, the endomorphism encoding the self-adjoint extension chosen. For particular examples, like the Friedrich's extension, the answer is easily extracted from the general result. In combination with \cite{BKD}, a closed expression for the determinant of an arbitrary self-adjoint extension of the full Laplace-type operator on the generalized cone can be obtained.Comment: 27 pages, 2 figures; to appear in Manuscripta Mathematic

Hydrographic data from the OPTOMA Program: OPTOMA11, 5-June-5 August, 1984

The six cruises and one aircraft flight comprising OPTOMA11 were undertaken in June, July and August 1984 to sample two subdomains of the California Current. This report presents the hydrographic data, acquired by XBT, AXBT and CTD casts, from the cruises and the flight.Research project "Ocean Prediction Through Observations, Modeling and Analysis" sponsored by the Physical Oceanography Program of the Office of Naval Research under Program Element 61153N.http://archive.org/details/hydrographicdata011wittN000148WR24051NAApproved for public release; distribution is unlimited

A Phylometagenomic Exploration of Oceanic Alphaproteobacteria Reveals Mitochondrial Relatives Unrelated to the SAR11 Clade

BACKGROUND: According to the endosymbiont hypothesis, the mitochondrial system for aerobic respiration was derived from an ancestral Alphaproteobacterium. Phylogenetic studies indicate that the mitochondrial ancestor is most closely related to the Rickettsiales. Recently, it was suggested that Candidatus Pelagibacter ubique, a member of the SAR11 clade that is highly abundant in the oceans, is a sister taxon to the mitochondrial-Rickettsiales clade. The availability of ocean metagenome data substantially increases the sampling of Alphaproteobacteria inhabiting the oxygen-containing waters of the oceans that likely resemble the originating environment of mitochondria. METHODOLOGY/PRINCIPAL FINDINGS: We present a phylogenetic study of the origin of mitochondria that incorporates metagenome data from the Global Ocean Sampling (GOS) expedition. We identify mitochondrially related sequences in the GOS dataset that represent a rare group of Alphaproteobacteria, designated OMAC (Oceanic Mitochondria Affiliated Clade) as the closest free-living relatives to mitochondria in the oceans. In addition, our analyses reject the hypothesis that the mitochondrial system for aerobic respiration is affiliated with that of the SAR11 clade. CONCLUSIONS/SIGNIFICANCE: Our results allude to the existence of an alphaproteobacterial clade in the oxygen-rich surface waters of the oceans that represents the closest free-living relative to mitochondria identified thus far. In addition, our findings underscore the importance of expanding the taxonomic diversity in phylogenetic analyses beyond that represented by cultivated bacteria to study the origin of mitochondria

Informational Gene Phylogenies Do Not Support a Fourth Domain of Life for Nucleocytoplasmic Large DNA Viruses

Mimivirus is a nucleocytoplasmic large DNA virus (NCLDV) with a genome size (1.2 Mb) and coding capacity ( 1000 genes) comparable to that of some cellular organisms. Unlike other viruses, Mimivirus and its NCLDV relatives encode homologs of broadly conserved informational genes found in Bacteria, Archaea, and Eukaryotes, raising the possibility that they could be placed on the tree of life. A recent phylogenetic analysis of these genes showed the NCLDVs emerging as a monophyletic group branching between Eukaryotes and Archaea. These trees were interpreted as evidence for an independent “fourth domain” of life that may have contributed DNA processing genes to the ancestral eukaryote. However, the analysis of ancient evolutionary events is challenging, and tree reconstruction is susceptible to bias resulting from non-phylogenetic signals in the data. These include compositional heterogeneity and homoplasy, which can lead to the spurious grouping of compositionally-similar or fast-evolving sequences. Here, we show that these informational gene alignments contain both significant compositional heterogeneity and homoplasy, which were not adequately modelled in the original analysis. When we use more realistic evolutionary models that better fit the data, the resulting trees are unable to reject a simple null hypothesis in which these informational genes, like many other NCLDV genes, were acquired by horizontal transfer from eukaryotic hosts. Our results suggest that a fourth domain is not required to explain the available sequence data